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Merge pull request #62 from bslakman/master
Radical solvation thermo groups
2 parents 89841fc + abb6027 commit c602f61

2 files changed

Lines changed: 386 additions & 2 deletions

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‎input/solvation/groups/abraham.py‎

Lines changed: 8 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -595,8 +595,14 @@
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2 H u0 {1,S}
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3 H u0 {1,S}
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""",
598-
solute = None,
599-
shortDesc = u"""""",
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solute = SoluteData(
599+
S = 0.175,
600+
B = 0.481,
601+
E = 0.085,
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L = 0.781,
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A = 0.0,
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),
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shortDesc = u"""Platts fragment 10 -NH2-aliphatic""",
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longDesc =
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u"""
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‎input/solvation/groups/radical.py‎

Lines changed: 378 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,378 @@
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#!/usr/bin/env python
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# encoding: utf-8
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name = "Radical Groups"
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shortDesc = u"Radical corrections to A"
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longDesc = u"""
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H-bonding parameter A should be modified for when we saturate
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radical molecules with hydrogens and look up the saturated
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structure.
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"""
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entry(
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index = 0,
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label = "R_rad",
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group =
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"""
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1 * R u1
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""",
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solute = None,
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shortDesc = u"""""",
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longDesc =
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u"""
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""",
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)
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entry(
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index = 1,
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label = "O_rad",
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group =
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"""
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1 * O u1 p2
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""",
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solute = None,
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shortDesc = u"""""",
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longDesc =
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u"""
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""",
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)
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entry(
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index = 2,
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label = "ROJ",
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group =
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"""
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1 * O u1 p2 c0 {2,S}
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2 R u0 {1,S}
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""",
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solute = SoluteData(
50+
S = 0.0,
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B = 0.0,
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E = 0.0,
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L = 0.0,
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A = -0.345,
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),
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shortDesc = u"""""",
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longDesc =
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u"""
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""",
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)
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entry(
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index = 3,
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label = "ROOJ",
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group =
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"""
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1 * O u1 p2 c0 {2,S}
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2 O u0 p2 {1,S} {3,S}
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3 R u0 {2,S}
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""",
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solute = SoluteData(
73+
S = 0.0,
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B = 0.0,
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E = 0.0,
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L = 0.0,
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A = -0.345,
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),
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shortDesc = u"""""",
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longDesc =
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u"""
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""",
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)
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entry(
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index = 4,
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label = "RC(O)OJ",
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group =
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"""
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1 * O u1 p2 c0 {2,S}
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2 C u0 p0 {1,S} {3,D} {4,S}
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3 O u0 p2 {2,D}
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4 R u0 {2,S}
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""",
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solute = SoluteData(
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S = 0.0,
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B = 0.0,
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E = 0.0,
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L = 0.0,
101+
A = -0.243,
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),
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shortDesc = u"""""",
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longDesc =
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u"""
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""",
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)
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entry(
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index = 5,
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label = "N3s_rad",
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group =
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"""
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1 * N3s u1 p1
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""",
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solute = SoluteData(
118+
S = 0.0,
119+
B = 0.0,
120+
E = 0.0,
121+
L = 0.0,
122+
A = -0.087,
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),
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shortDesc = u"""""",
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longDesc =
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u"""
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""",
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)
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entry(
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index = 6,
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label = "N3_pyrrole",
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group =
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"""
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1 * N3s u1 p1 {2,S} {3,S}
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2 Cb u0 {1,S} {4,B}
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3 Cb u0 {1,S} {5,B}
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4 Cb u0 {2,B} {5,B}
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5 Cb u0 {3,B} {4,B}
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""",
142+
solute = SoluteData(
143+
S = 0.0,
144+
B = 0.0,
145+
E = 0.0,
146+
L = 0.0,
147+
A = -0.371,
148+
),
149+
shortDesc = u"""""",
150+
longDesc =
151+
u"""
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""",
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)
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entry(
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index = 7,
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label = "phenoxy",
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group =
160+
"""
161+
1 * O u1 p2 c0 {2,S}
162+
2 Cb u0 {1,S}
163+
""",
164+
solute = SoluteData(
165+
S = 0.0,
166+
B = 0.0,
167+
E = 0.0,
168+
L = 0.0,
169+
A = -0.543,
170+
),
171+
shortDesc = u"""""",
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longDesc =
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u"""
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""",
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)
177+
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entry(
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index = 8,
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label = "N3_aniline",
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group =
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"""
183+
1 * N3s u1 p1 c0 {2,S} {3,S}
184+
2 H u0 p0 c0 {1,S}
185+
3 Cb u0 {1,S} {4,B} {5,B}
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4 Cb u0 {3,B} {6,B}
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5 Cb u0 {3,B} {7,B}
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6 Cb u0 {4,B} {8,B}
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7 Cb u0 {5,B} {8,B}
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8 Cb u0 {6,B} {7,B}
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""",
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solute = SoluteData(
193+
S = 0.0,
194+
B = 0.0,
195+
E = 0.0,
196+
L = 0.0,
197+
A = -0.247,
198+
),
199+
shortDesc = u"""""",
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longDesc =
201+
u"""
202+
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""",
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)
205+
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entry(
207+
index = 9,
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label = "N3_amide_pri",
209+
group =
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"""
211+
1 * N3s u1 p1 c0 {2,S} {3,S}
212+
2 H u0 p0 c0 {1,S}
213+
3 CO u0 {1,S} {4,D}
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4 O u0 p2 {3,D}
215+
""",
216+
solute = SoluteData(
217+
S = 0.0,
218+
B = 0.0,
219+
E = 0.0,
220+
L = 0.0,
221+
A = -0.275,
222+
),
223+
shortDesc = u"""""",
224+
longDesc =
225+
u"""
226+
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""",
228+
)
229+
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entry(
231+
index = 10,
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label = "N3_amide_sec",
233+
group =
234+
"""
235+
1 * N3s u1 p1 c0 {2,S} {3,S}
236+
2 R!H u0 {1,S}
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3 CO u0 {1,S} {4,D}
238+
4 O u0 p2 {3,D}
239+
""",
240+
solute = SoluteData(
241+
S = 0.0,
242+
B = 0.0,
243+
E = 0.0,
244+
L = 0.0,
245+
A = -0.281,
246+
),
247+
shortDesc = u"""""",
248+
longDesc =
249+
u"""
250+
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""",
252+
)
253+
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entry(
255+
index = 11,
256+
label = "N3_amide_aromatic",
257+
group =
258+
"""
259+
1 * N3s u1 p1 c0 {2,S} {3,S}
260+
2 [Cb,N3b] u0 {1,S}
261+
3 CO u0 {1,S} {4,D}
262+
4 O u0 p2 {3,D}
263+
""",
264+
solute = SoluteData(
265+
S = 0.0,
266+
B = 0.0,
267+
E = 0.0,
268+
L = 0.0,
269+
A = 0.091,
270+
),
271+
shortDesc = u"""""",
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longDesc =
273+
u"""
274+
275+
""",
276+
)
277+
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entry(
279+
index = 12,
280+
label = "N3_urea_pri",
281+
group =
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"""
283+
1 * N3s u1 p1 c0 {2,S} {3,S}
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2 R!H u0 p0 c0 {1,S}
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3 CO u0 {1,S} {4,D} {5,S}
286+
4 O u0 p2 {3,D}
287+
5 N3s u0 p1 {3,S} {6,S}
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6 H u0 p0 c0 {5,S}
289+
""",
290+
solute = SoluteData(
291+
S = 0.0,
292+
B = 0.0,
293+
E = 0.0,
294+
L = 0.0,
295+
A = 0.0825,
296+
),
297+
shortDesc = u"""""",
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longDesc =
299+
u"""
300+
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""",
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)
303+
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entry(
305+
index = 13,
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label = "N3_urea_sec",
307+
group =
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"""
309+
1 * N3s u1 p1 c0 {2,S} {3,S}
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2 R!H u0 p0 c0 {1,S}
311+
3 CO u0 {1,S} {4,D} {5,S}
312+
4 O u0 p2 {3,D}
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5 N3s u0 p1 {3,S} {6,S} {7,S}
314+
6 R!H u0 {5,S}
315+
7 R!H u0 {5,S}
316+
""",
317+
solute = SoluteData(
318+
S = 0.0,
319+
B = 0.0,
320+
E = 0.0,
321+
L = 0.0,
322+
A = 0.119,
323+
),
324+
shortDesc = u"""""",
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longDesc =
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u"""
327+
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""",
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)
330+
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entry(
332+
index = 14,
333+
label = "N3d_guanidine",
334+
group =
335+
"""
336+
1 Cd u0 {2,D} {3,S} {4,S}
337+
2 * N3d u1 {1,D}
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3 N3s u0 {1,S} {5,S} {6,S}
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4 N3s u0 {1,S} {7,S} {8,S}
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5 H u0 {3,S}
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6 H u0 {3,S}
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7 H u0 {4,S}
343+
8 H u0 {4,S}
344+
""",
345+
solute = SoluteData(
346+
S = 0.0,
347+
B = 0.0,
348+
E = 0.0,
349+
L = 0.0,
350+
A = -0.17
351+
),
352+
shortDesc = u"""""",
353+
longDesc =
354+
u"""
355+
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""",
357+
)
358+
tree(
359+
"""
360+
L1: R_rad
361+
L2: O_rad
362+
L3: ROJ
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L4: RC(O)OJ
364+
L4: ROOJ
365+
L4: phenoxy
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L2: N3s_rad
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L3: N3_pyrrole
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L3: N3_aniline
369+
L3: N3_amide_pri
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L4: N3_urea_pri
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L3: N3_amide_sec
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L4: N3_urea_pri
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L4: N3_urea_sec
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L4: N3_amide_aromatic
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L2: N3d_guanidine
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"""
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)
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